Conserved Protein Domain Family
TM_Y_betaCoV_Nsp3_C

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cd21713: TM_Y_betaCoV_Nsp3_C 
C-terminus of betacoronavirus non-structural protein 3, including transmembrane and Y domains
This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In SARS-CoV and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain.
Statistics
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PSSM-Id: 409661
Aligned: 5 rows
Threshold Bit Score: 830.216
Created: 28-Apr-2020
Updated: 25-Oct-2021
Structure
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Aligned Rows:
 
TM1 [structuralTM2 [structural
Feature 1:TM1 [structural motif]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         ######################                                                          
QHD43415     2232 WFLLLSVCLGSLIYSTAALGVLm------------------SNLGMPSYCTGYREGYLNSTnv-------tiATYCTg-S 2285 Severe acute ...
P0C6T6       2084 YIWFVWTCLTICGVWLSEPYAP-------------------SLVTRFKYFLGIVMPCDYVLv----------NETGT--G 2132 Rousettus bat...
P0C6V0       2282 VSRGFFLVATVFLLWFNFLYANvilsdfylpnigplptfvgQIVAWFKTTFGVSTICDFYQvtdl----gyrSSFCNg-S 2356 Murine hepati...
YP_009072438 2353 RVFALATCIAAILYMAMFVYLFfdiwls--------kanvwTDVQTLKDNFGLGTVCDKFQtaynnsgiydaTEYCTgkS 2424 Bat Hp-betaco...
AVV62536     2203 LRLLLVLCTTGLLLSSIYHLYIfnqvvssda-mlddvtgfmAIYKEIRSYLHITSACDGLArdyra-nsfdiSNFCAnrS 2280 Middle East r...
Feature 1                                                                                         
QHD43415     2286 IPCSVCLSGLDSLDTYPSleTIQITISSFKWDLta--fgLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFIs--N 2361 Severe acute ...
P0C6T6       2133 WLHHLCMAGMDSLDYPALr-MQQHRYGSPYNYTyi---lMLLEAFFAYLLYTPALPIVGILAVLHLIVLYLPIPLG---N 2205 Rousettus bat...
P0C6V0       2357 MVCELCFSGFDMLDNYDAinVVQHVVDRRLSFDyislfkLVVELVIGYSLYTVCFYPLFVLIGMQLLTTWLPEFFMletM 2436 Murine hepati...
YP_009072438 2425 FMCSLCLRGMDSLNFYTElsTSQKTVSWSSFDFsn--inTAAEWCLAYLLYTKMFVVLLATAIFQWFAVYFGLYLTq--S 2500 Bat Hp-betaco...
AVV62536     2281 ALCKWCLLGQDSITHYSAlkMVQTHISHYVLNVdw--lwFALELLFAYVMYTAAFNWVLLACTLQYFFSQTSLFVDw-rS 2357 Middle East r...
Feature 1                                                                                         
QHD43415     2362 SWLMWLIINLVq-mAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANG 2440 Severe acute ...
P0C6T6       2206 SWLVVFLYYIIr-lVPFTSMLRMYIVIAFLWLCYKGFLHVRYGCNNVACLMCYKKNVAKRIECSTVVNGVKRMFYVNANG 2284 Rousettus bat...
P0C6V0       2437 HWSARLFVFVAn-mLPAFTLLRFYIVVTAMYKVYCLCRHVMYGCSKPGCLFCYKRNRSVRVKCSTVVGGSLRYYDVMANG 2515 Murine hepati...
YP_009072438 2501 SWLMWTMVRVIs-lVPTSILVRMYIYCASFYFVYRAYVHVVSGCQDTRCLMCYKRNLARRVECHTVVQGSRKSFYVHANG 2579 Bat Hp-betaco...
AVV62536     2358 YNYVVSCIYLLfthIPLDGLVRIYNVLACLWFLRKFYNHAINGCKDTACLLCYKRNRLTRVEASTVVCGTKRTFYIAANG 2437 Middle East r...
Feature 1                                                                                         
QHD43415     2441 GKgFCKLHNWNCVNCDTFCAGSTFISDEVARDLSlqfKRPINPTDQSSYIVDSVTVknGSIHLYFDKAGQKtYERHSLSH 2520 Severe acute ...
P0C6T6       2285 GThFCTKHNWNCVSCDTYTVDSTFICRQVALDLSaqfKRPIIHTDEAYYEVTSVEVrnGYVYCYFESDGQRsYERFPMDA 2364 Rousettus bat...
P0C6V0       2516 GTgFCTKHQWNCLNCNSWKPGNTFITHEAAADLSkelKRPVNPTDSAYYSVTEVKQvgCSMRLFYERDGQRvYDDVNASL 2595 Murine hepati...
YP_009072438 2580 GTgFCEKHAWNCINCDSYGPGNTFICDEVAVDLSttfKRPVKPTDKSHYFVDSVEVkdTFVHLYYSKNDTRvYDRYPLSV 2659 Bat Hp-betaco...
AVV62536     2438 GTsFCCRHNWNCVDCDTAGIGNTFICEEVANDLTtglRRLIKPTDRSHYYVNSVEVkdTVVQLNYTRDGQVcYERFSLCY 2517 Middle East r...
Feature 1                                                                                         
QHD43415     2521 FVNLDNLRANNTKgslp----invIVFDGKSKCEESsaKSASVYYSQLMCQPILLLDQALVSDVGDSAevavKMFDAYVN 2596 Severe acute ...
P0C6T6       2365 FTNVSKLHYSELKgaap---afnvLVFDATNRIEENavKTAAIYYAQLACKPILLVDKRMVGVVGDDAtiarAMFEAYAQ 2441 Rousettus bat...
P0C6V0       2596 FVDMNGLLHSKVKgvp------etHVVVVENEADKAgfLGAAVFYAQSLYRPMLMVEKKLITTANTGLsvsrTMFDLYVD 2669 Murine hepati...
YP_009072438 2660 FSSVDFLKLANIKtmps----tnvLVFDASNKTEENttVAASVYYSQLCCQPMLLIEQKLLSNIGDATevskKMLDAYIE 2735 Bat Hp-betaco...
AVV62536     2518 FSNLDKLKFKEVCksttgipehnfIIYDASDRGQENlaRSACVYYSQVLCKPILLVDSNLVTSVGDSTeiatKMFDSFVN 2597 Middle East r...
Feature 1                                                                                         
QHD43415     2597 TFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGF--VDSDVETKDVVECLKlsHQSDIEVTGDSCNNYM 2674 Severe acute ...
P0C6T6       2442 NYLLKYSIAMDKVKHLYSTALQQISSGMTVESVLKVFVGSTRAEAkdLESDVDTNDLVSCIRlcHQEGWEWTTDSWNNLV 2521 Rousettus bat...
P0C6V0       2670 SLLNVLDVDRKSLTSFVNAAHNSLKEGVQLEQVMDTFIGCARRKCa-IDSDVETKSITKSVMsaVNAGVDFTDESCNNLV 2748 Murine hepati...
YP_009072438 2736 KFMSTFGVTMEKLKTFVSAAKNSLNDGVPLEKVLKEFVAAAKQNC--AETDVEADSIVNALQltFKDDVDITKDSYNDFV 2813 Bat Hp-betaco...
AVV62536     2598 SFVSLYNVTRDRLEKLISTARDGLKRGENLQPILKTFIDAARGPAg-VESDIDTGDIVDAVQyaHKHDIQLTTEGYNNYV 2676 Middle East r...
Feature 1                                                                                         
QHD43415     2675 LTYNKVENmtprDLGACIDCSARHINAQVAKSHNIALIWNvkdFMSLSEQLRKQIRSAAKKNNLpFKLTCATTRQVVNVV 2754 Severe acute ...
P0C6T6       2522 PTYIKQDTlstlEVGQFMTANAKYVNANIAKGAAVNLIWRyadFIKLSESMRRQLKVAARKTGLnLLVTTSSLKADVPCM 2601 Rousettus bat...
P0C6V0       2749 PTYVKSDTivaaDLGVLIQNNAKHVQANVAKAANVACIWSvdaFNQLSADLQHRLRKACSKTGLkIKLTYNKQEANVPIL 2828 Murine hepati...
YP_009072438 2814 LTYNKVDSmtpyDLGVCIEVGARHVNANVAKANAAALIWNidhYLLLSESFRRQIRSSARKNGLqFKLTCSKNRQVTPFL 2893 Bat Hp-betaco...
AVV62536     2677 PSYVKPDSiatsDLGSLIDSNAASVNPANMRNANGACVWNaaaYLKLSDALKRQVRIACRKCNLnFRLTTSKLRACDNIL 2756 Middle East r...
Feature 1                 
QHD43415     2755 TTKIALKG 2762 Severe acute respiratory syndrome coronavirus 2
P0C6T6       2602 VTPFKIIG 2609 Rousettus bat coronavirus HKU9
P0C6V0       2829 TTPFSLKG 2836 Murine hepatitis virus strain A59
YP_009072438 2894 TTKIMFSG 2901 Bat Hp-betacoronavirus/Zhejiang2013
AVV62536     2757 SVRFSATK 2764 Middle East respiratory syndrome-related coronavirus

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